Build from source had failed (similar to #39293)

[alibayeh]

Julia version: 1.9.3 - installed via released package from Julia website (I tried older versions and I got same error) OS: Linux 6.5.2 (with zen kernel) Arch: x86 Glibc version: 2.38 Output:

» julia
┌ Warning: CHOLMOD version incompatibility
│
│ Julia was compiled with CHOLMOD version 3.0.14. It is
│ currently linked with version 4.0.4.
│ This might cause Julia to terminate when working with
│ sparse matrix factorizations, e.g. solving systems of
│ equations with \.
│
│ It is recommended that you use Julia with the same major
│ version of CHOLMOD as the one used during the build, or
│ download the generic binaries from www.julialang.org,
│ which ship with the correct versions of all dependencies.
└ @ SparseArrays.CHOLMOD /opt/julia/share/julia/stdlib/v1.9/SparseArrays/src/solvers/cholmod.jl:198
[1]    175797 segmentation fault (core dumped)  julia

Moreover I got this error when I tried to build Julia from source with/without USE_BINARYBUILDER=0,

» gcc --version                                                                                                                                                                               1 ↵
gcc (GCC) 12.3.0
»
» git status
HEAD detached at v1.9.3
nothing to commit, working tree clean
»
» make -j8
.
.
.
    LINK usr/lib/libjulia-internal.so.1.9
    LINK usr/lib/libjulia-internal.so.1
    LINK usr/lib/libjulia-internal.so
    LINK usr/lib/libjulia-codegen.so.1.9
    LINK usr/lib/libjulia-codegen.so.1
    LINK usr/lib/libjulia-codegen.so
    JULIA usr/lib/julia/corecompiler.ji
make[1]: *** [sysimage.mk:61: /tmp/julia/usr/lib/julia/corecompiler.ji] Error 135
make: *** [Makefile:84: julia-sysimg-ji] Error 2
»
» ls /tmp/julia/usr/lib/julia/corecompiler.ji                                                                                                                                                 2 ↵
ls: cannot access '/tmp/julia/usr/lib/julia/corecompiler.ji': No such file or directory

[oscardssmith]

this sounds like a possible ld_preload issue

[alibayeh]

this sounds like a possible ld_preload issue

» ls /opt/julia/lib/julia/libcholmod.so.3.0.14
/opt/julia/lib/julia/libcholmod.so.3.0.14
» export LD_PRELOAD=$LD_PRELOAD:/opt/julia/lib/julia/; julia                                                                                                                                139 ↵
ERROR: ld.so: object '/opt/julia/lib/julia' from LD_PRELOAD cannot be preloaded (cannot read file data): ignored.
ERROR: ld.so: object '/opt/julia/lib/julia' from LD_PRELOAD cannot be preloaded (cannot read file data): ignored.
ERROR: ld.so: object '/opt/julia/lib/julia/' from LD_PRELOAD cannot be preloaded (cannot read file data): ignored.
┌ Warning: CHOLMOD version incompatibility
│
│ Julia was compiled with CHOLMOD version 3.0.14. It is
│ currently linked with version 4.0.4.
│ This might cause Julia to terminate when working with
│ sparse matrix factorizations, e.g. solving systems of
│ equations with \.
│
│ It is recommended that you use Julia with the same major
│ version of CHOLMOD as the one used during the build, or
│ download the generic binaries from www.julialang.org,
│ which ship with the correct versions of all dependencies.
└ @ SparseArrays.CHOLMOD /opt/julia/share/julia/stdlib/v1.9/SparseArrays/src/solvers/cholmod.jl:198
[1]    179981 segmentation fault (core dumped)  julia

[oscardssmith]

I probably should have been more specific. The problem is likely that there is something in the path, not the lack of something (as in https://github.com/JuliaLang/julia/issues/48647 for example). Specifically, see if launching with LD_LIBRARY_PATH="" or LD_PRELOAD="" fixes it.

[alibayeh]

I probably should have been more specific. The problem is likely that there is something in the path, not the lack of something (as in #48647 for example). Specifically, see if launching with LD_LIBRARY_PATH="" or LD_PRELOAD="" fixes it.

Thank you. The problem is solved. Do you have any idea about the build error?

[oscardssmith]

not at all. That's really weird.

[alibayeh]

I found similar solved issue #39293 for Arm32bit Arch.

[M-S-Jacobs2727]

Same thing happened to me; compiling v1.9.4 on Fedora 39 with gcc 13.2.1 I got the error

    ...
    JULIA usr/lib/julia/corecompiler.ji
make[1]: *** [sysimage.mk:61: /home/jacobs/software/julia/usr/lib/julia/corecompiler.ji] Error 139
make: *** [Makefile:84: julia-sysimg-ji] Error 2

Running again with LD_LIBRARY_PATH="" make allowed the build to complete (LD_PRELOAD="" make did not).

Additionally, when running make testall, I got the following output:

Whitespace check found no issues.
cp /home/jacobs/software/julia/usr/lib/julia/sys.so /home/jacobs/software/julia/local.so
/home/jacobs/software/julia/usr/bin/julia -J /home/jacobs/software/julia/local.so -e 'true'
rm /home/jacobs/software/julia/local.so
    JULIA test/all
make[1]: *** [Makefile:25: all] Segmentation fault (core dumped)
make: *** [Makefile:601: testall] Error 2

and again running LD_LIBRARY_PATH="" make testall fixed it. I'll update this comment if I find something similar.

Update: As I thought, once the installation and tests were completed, I tried installing a package in the REPL with

julia> ]add JuliaFormatter
Segmentation fault (core dumped)

but running the REPL with LD_LIBRARY_PATH="" julia installed it correctly. I'll make an alias as a workaround, but any other advice would be appreciated.